Figure 2

Read to gene assignment confidence. Reads are assigned to genes with three different levels. Proximal (P) reads are those mapping close to gene boundaries, Genic (G) reads overlap gene coordinates, Transcript (T) reads show ungapped matches with RefSeq transcripts annotated as part of the gene model, Extragenic reads (O) represent reads falling outside gene coordinates beyond the defined "surrounding" region. Both the extension of the "surrounding region" (thin red line labeled as "a" in figure) and the minimum overlap with gene mapping region to classify reads as "G" (thin blue line "b") can be defined by the user.